Computational modeling of realistic cell membranes
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …
[HTML][HTML] Lipid–protein interactions in biological membranes: a structural perspective
AG Lee - Biochimica et Biophysica Acta (BBA)-Biomembranes, 2003 - Elsevier
Lipid molecules bound to membrane proteins are resolved in some high-resolution
structures of membrane proteins. An analysis of these structures provides a framework …
structures of membrane proteins. An analysis of these structures provides a framework …
A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems
Knowledge of the structure and dynamics of membranes has traditionally been fragmentary
at the atomic level. This is due partly to the fluid character of membranes under physiological …
at the atomic level. This is due partly to the fluid character of membranes under physiological …
Texts in Computational Science and Engineering
The rapid development of parallel computing systems made it possible to recreate and
predict physical processes on computers. Nowadays, computer simulations complement …
predict physical processes on computers. Nowadays, computer simulations complement …
Setting up and running molecular dynamics simulations of membrane proteins
C Kandt, WL Ash, DP Tieleman - Methods, 2007 - Elsevier
Molecular dynamics simulations have become a popular and powerful technique to study
lipids and membrane proteins. We present some general questions and issues that should …
lipids and membrane proteins. We present some general questions and issues that should …
CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications
Molecular dynamics simulations of membranes and membrane proteins serve as
computational microscopes, revealing coordinated events at the membrane interface. As G …
computational microscopes, revealing coordinated events at the membrane interface. As G …
Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 Å resolution
Abstract Background: Bacteriorhodopsin (bR) from Halobacterium salinarum is a proton
pump that converts the energy of light into a proton gradient that drives ATP synthesis. The …
pump that converts the energy of light into a proton gradient that drives ATP synthesis. The …
Bioenergetics of the Archaea
G Schäfer, M Engelhard… - … and molecular biology …, 1999 - Am Soc Microbiol
In the late 1970s, on the basis of rRNA phylogeny, Archaea (archaebacteria) was identified
as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a …
as a distinct domain of life besides Bacteria (eubacteria) and Eucarya. Though forming a …
A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer
DP Tieleman, HJC Berendsen - Biophysical journal, 1998 - cell.com
In this paper we study the properties of pores formed by OmpF porin from Escherichia coli,
based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl …
based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl …
Effective energy function for proteins in lipid membranes
T Lazaridis - Proteins: Structure, Function, and Bioinformatics, 2003 - Wiley Online Library
A simple extension of the EEF1 energy function to heterogeneous membrane‐aqueous
media is proposed. The extension consists of (a) development of solvation parameters for a …
media is proposed. The extension consists of (a) development of solvation parameters for a …